| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:31:27 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the GeneticsDesign package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 703/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
The R Genetics Project
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | ERROR | OK | |||||||||
| Package: GeneticsDesign |
| Version: 1.58.0 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneticsDesign.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings GeneticsDesign_1.58.0.tar.gz |
| StartedAt: 2021-05-06 03:04:05 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 03:04:32 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 26.8 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: GeneticsDesign.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneticsDesign.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings GeneticsDesign_1.58.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/GeneticsDesign.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GeneticsDesign/DESCRIPTION' ... OK
* this is package 'GeneticsDesign' version '1.58.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'GeneticsDesign' can be installed ... WARNING
Found the following significant warnings:
Warning: newline within quoted string at GPC.Rd:38
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEz9dyj/R.INSTALL15684a382180/GeneticsDesign/man/GPC.Rd:40: unexpected section header '\value'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEz9dyj/R.INSTALL15684a382180/GeneticsDesign/man/GPC.Rd:49: unexpected UNKNOWN '\item'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEz9dyj/R.INSTALL15684a382180/GeneticsDesign/man/GPC.Rd:51: unexpected UNKNOWN '\item'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEz9dyj/R.INSTALL15684a382180/GeneticsDesign/man/GPC.Rd:53: unexpected UNKNOWN '\item'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEz9dyj/R.INSTALL15684a382180/GeneticsDesign/man/GPC.Rd:49: All text must be in a section
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEz9dyj/R.INSTALL15684a382180/GeneticsDesign/man/GPC.Rd:51: All text must be in a section
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEz9dyj/R.INSTALL15684a382180/GeneticsDesign/man/GPC.Rd:53: All text must be in a section
Warning: Package 'GeneticsDesign' is deprecated and will be removed from
See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/GeneticsDesign.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
power.casectrl.plot: warning in matrix(NA, nc = J, nr = length(p)):
partial argument match of 'nr' to 'nrow'
power.casectrl.plot: warning in matrix(NA, nc = J, nr = length(p)):
partial argument match of 'nc' to 'ncol'
pw: warning in matrix(c(1, pi, pi, 1), nr = 2): partial argument match
of 'nr' to 'nrow'
pw: warning in matrix(c(sd1^2, sd1 * sd2, sd1 * sd2, sd2^2), nr = 2):
partial argument match of 'nr' to 'nrow'
simu.genotype.conti: warning in matrix(c(1, pi, pi, 1), nr = 2):
partial argument match of 'nr' to 'nrow'
simu.genotype.conti: warning in matrix(c(sd1^2, sd1 * sd2, sd1 * sd2,
sd2^2), nr = 2): partial argument match of 'nr' to 'nrow'
* checking Rd files ... WARNING
prepare_Rd: newline within quoted string at GPC.Rd:38
prepare_Rd: man/GPC.Rd:40: unexpected section header '\value'
prepare_Rd: man/GPC.Rd:49: unexpected UNKNOWN '\item'
prepare_Rd: man/GPC.Rd:51: unexpected UNKNOWN '\item'
prepare_Rd: man/GPC.Rd:53: unexpected UNKNOWN '\item'
prepare_Rd: GPC.Rd:49: All text must be in a section
prepare_Rd: GPC.Rd:51: All text must be in a section
prepare_Rd: GPC.Rd:53: All text must be in a section
prepare_Rd: power.genotype.conti.Rd:36-38: Dropping empty section \details
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Paragraph ended before \Rd@code was complete.
<to be read again>
\par
l.219
* checking PDF version of manual without hyperrefs or index ... ERROR
* DONE
Status: 1 ERROR, 3 WARNINGs, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.12-bioc/meat/GeneticsDesign.Rcheck/00check.log'
for details.
GeneticsDesign.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/GeneticsDesign_1.58.0.tar.gz && rm -rf GeneticsDesign.buildbin-libdir && mkdir GeneticsDesign.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GeneticsDesign.buildbin-libdir GeneticsDesign_1.58.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL GeneticsDesign_1.58.0.zip && rm GeneticsDesign_1.58.0.tar.gz GeneticsDesign_1.58.0.zip
###
##############################################################################
##############################################################################
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 16800 100 16800 0 0 946k 0 --:--:-- --:--:-- --:--:-- 1025k
install for i386
* installing *source* package 'GeneticsDesign' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
Warning: newline within quoted string at GPC.Rd:38
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEz9dyj/R.INSTALL15684a382180/GeneticsDesign/man/GPC.Rd:40: unexpected section header '\value'
Warning: newline within quoted string at GPC.Rd:38
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEz9dyj/R.INSTALL15684a382180/GeneticsDesign/man/GPC.Rd:49: unexpected UNKNOWN '\item'
Warning: newline within quoted string at GPC.Rd:38
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEz9dyj/R.INSTALL15684a382180/GeneticsDesign/man/GPC.Rd:51: unexpected UNKNOWN '\item'
Warning: newline within quoted string at GPC.Rd:38
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEz9dyj/R.INSTALL15684a382180/GeneticsDesign/man/GPC.Rd:53: unexpected UNKNOWN '\item'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEz9dyj/R.INSTALL15684a382180/GeneticsDesign/man/GPC.Rd:49: All text must be in a section
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEz9dyj/R.INSTALL15684a382180/GeneticsDesign/man/GPC.Rd:49: All text must be in a section
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEz9dyj/R.INSTALL15684a382180/GeneticsDesign/man/GPC.Rd:49: All text must be in a section
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEz9dyj/R.INSTALL15684a382180/GeneticsDesign/man/GPC.Rd:49: All text must be in a section
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEz9dyj/R.INSTALL15684a382180/GeneticsDesign/man/GPC.Rd:51: All text must be in a section
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEz9dyj/R.INSTALL15684a382180/GeneticsDesign/man/GPC.Rd:51: All text must be in a section
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEz9dyj/R.INSTALL15684a382180/GeneticsDesign/man/GPC.Rd:51: All text must be in a section
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEz9dyj/R.INSTALL15684a382180/GeneticsDesign/man/GPC.Rd:51: All text must be in a section
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEz9dyj/R.INSTALL15684a382180/GeneticsDesign/man/GPC.Rd:53: All text must be in a section
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEz9dyj/R.INSTALL15684a382180/GeneticsDesign/man/GPC.Rd:53: All text must be in a section
*** installing help indices
converting help for package 'GeneticsDesign'
finding HTML links ... done
GPC html
GeneticPower.Quantitative.Numeric html
depreciated html
gregorius html
power.genotype.conti html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'GeneticsDesign' is deprecated and will be removed from
Bioconductor version 3.13
** testing if installed package can be loaded from final location
Warning: Package 'GeneticsDesign' is deprecated and will be removed from
Bioconductor version 3.13
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'GeneticsDesign' ...
** testing if installed package can be loaded
Warning: Package 'GeneticsDesign' is deprecated and will be removed from
Bioconductor version 3.13
* MD5 sums
packaged installation of 'GeneticsDesign' as GeneticsDesign_1.58.0.zip
* DONE (GeneticsDesign)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'GeneticsDesign' successfully unpacked and MD5 sums checked
|
GeneticsDesign.Rcheck/examples_i386/GeneticsDesign-Ex.timings
|
GeneticsDesign.Rcheck/examples_x64/GeneticsDesign-Ex.timings
|